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What type of integration are you after with Exchange and Lotus? IMAP? Unified Messaging? Keep in mind, there are currently no options for unified messaging between UC and Lotus Domino. Also, unified messaging with Exchange was introduced in version 8.5 and higher. There are no requirements as far as splitting up connectivity from Exchange and Lotus to two different servers.

As Bradford notes, Cisco does not support using Lotus Domino as a message store for Unity Connection. Instead, your best integration option is likely to be using Cisco's Unified Messaging plug-in for Lotus Sametime. This allows you to display voice-mail from Unity Connection in the Lotus Notes 8.5.x sidebar (or within the standalone Sametime 8.5.x client).

The plug-in works with Unity Connection versions 2.1 through 8.6 (also Unity 5.0 through 8.0). The release notes are here. As the plug-in just requires IMAP access to the message store, there's no restriction on you also using other clients to display Unity Connections messages.